This study presents petrochemical and boron isotope compositions of tourmalines from the fertile (No. 3) and relatively barren (No. 1, 2b) pegmatite in the Koktokay pegmatitic rare-metal deposit, to better understand the influence of external contamination on pegmatite mineralization and the source of these pegmatites. There are four types of tourmalines that have been studied: (1) tourmaline in the tourmaline-mica nest of pegmatite No. 1 (Tur-N); (2) tourmalines in the comb-like structure of pegmatite No. 1 (Tur-C1), 2b (Tur-C2), and 3 (Tur-C3), respectively. Tur-N tourmaline is heterogeneous in backscattered electron (BSE) images, Tur-C1 and Tur-C2 appear to be homogenous crystals, while Tur-C3 exhibits to have a complicated zonal structure. These tourmalines are members of the alkali group tourmalines representing mostly dravite-schorl solid solutions. Tur-N contains the lowest Ca content. There is a general increase in the contents of Mg and Ca from Tur-C1 to Tur-C3, implying that the pegmatite melt was contaminated by the host rock (metagabbro) during the emplacement. The contamination's diffusive influx of Mg, Ca, and Fe components into the pegmatite melt impelled the crystallization of tourmaline during the emplacement, which subsequently triggered the deposition of rare element minerals. The external contamination implies that the closed system of melt is extremely favorable for the enrichment and mineralization of rare elements in the pegmatitic rare-metal deposit. The boron isotopes vary slightly among the four types of tourmalines. The B-isotope composition of Tur-C3 is the heaviest (–11.63 ± 0.05 ‰ to –13.16 ± 0.05 ‰), followed by Tur-C1 (–12.29 ± 0.06 ‰ to –12.93 ± 0.05 ‰) and Tur-C2 (–12.51 ± 0.05 ‰ to –13.21 ± 0.05 ‰), Tur-N contains the lowest δ11B value (–13.20 ± 0.05 ‰ to –13.76 ± 0.05 ‰). Synthesized with the previous research results, we hold that the boron isotope of tourmaline (Tur-C3) in the comb-like structure of No. 3 pegmatite might represent the isotope composition of its initial magma, indicating that the tourmaline and associated pegmatite may derive from the melting of clastic sedimentary rock from the Habahe Group forming in Mid Ordovician to Early Devonian in the Chinese Altay orogenic belt.